Welcome to StangNet, myillwillinc!!!
Actually there was only a small hood clearance problem when 50mustangsandsuperfords mag did this swap back in the 11-03 issue. Although the intake, plenum and TB fit under the stock hood, the linkage required a hole to be cut on the inner liner of the hood, but nothing to the outer skin. They fabricated adapters to allow the 4.6 manifold to fit onto the 5.4. This is a great article.
On the dyno, the stock motor generated 205 RWHP/254 FTLB TQE. The 5.4, basically stock as a rock, generated 215 RWHP/306 FTLB TQE (at 2500 RPMs - hey, it is essentially a truck motor!) With a bit of tuning, they got 226 RWHP and 329 FTLB TQE (still at 2500), but it was obvious the long runners of the manifold (as well as the cams' grinds) were limiting the potential power. HP gains down low were as large as 44 RWHP over the 4.6.
They used a 5.4 motor out of a wrecked 00 E-150 van with only 4k miles - $1150. They sold the 4.6 (with 98K on it) for $450, leaving a net bill of $700. Plus another $200 or so for various gaskets and billet aluminum for the adapters.